Matze88:
I'm not one of the experts, so I can answer only one of your questions. No matter what you try, the original firmware on the iRiver H300 series will not recognize, and will not boot from your CF card. It does not have the capability. "Check HDD" and "Check HDD connection" are its error messages for a dead or missing hard drive. Hence you will need to keep around your 20 GB hard drive in case you ever need to reflash the firmware.
I have been fiddling around with the CF mod for about the last year, following a similar path to yours. Some of the cards I have used have worked perfectly, and others not. I started with fiscal caution, trying out an 8 GB Transcend 133X. When it worked perfectly, I splurged on a 32 GB Transcend 133x. Though the same make, the bigger card has been erratic. It seems to consistently freeze if I try to fast-forward or fast-reverse through a song, and if I finish playing sudoku and try to go to a song. Sometimes it would work if I waited for the drive search icon to go off between key clicks. But not always.
It was all too disappointing. So a month ago I bought a 32 GB RiData 233X, since Wintermute had reported success with it. And, it has worked perfectly for me as well.